Structural and functional characterization of Escherichia coli UMP kinase in complex with its allosteric regulator GTP.
Bacterial UMP kinases are essential enzymes involved in the multistep synthesis of UTP. They are hexamers regulated by GTP (allosteric activator) and UTP (inhibitor). We describe here the 2.8 angstroms crystal structure of Escherichia coli UMP kinase bound to GTP. The GTP-binding site, situated at 15 angstroms from the UMP-binding site and at 24 angstroms from the ATP-binding site, is delineated by two contiguous dimers. The overall structure, as compared with those bound to UMP, UDP, or UTP, shows a rearrangement of its quaternary structure: GTP induces an 11 degrees opening of the UMP kinase dimer, resulting in a tighter dimer-dimer interaction. A nucleotide-free UMP kinase dimer has an intermediate opening. Superposition of our structure with that of archaeal UMP kinases, which are also hexamers, shows that a loop appears to hamper any GTP binding in archeal enzymes. This would explain the absence of activating effect of GTP on this group of UMP kinases. Among GTP-binding residues, the Asp-93 is the most conserved in bacterial UMP kinases. In the previously published structures of E. coli UMP kinase, this residue was shown to be involved in hydrogen bonds between the subunits of a dimer. Its substitution by an alanine decreases the cooperativity for UTP binding and suppresses the reversal by GTP of UTP inhibition. This demonstrates that the previously described mutual exclusion of these two nucleotides is mediated by Asp-93.
Meyer
Philippe
P
Laboratoire d'Enzymologie et de Biochimie Structurales, CNRS, UPR 3082, 91198 Gif-sur-Yvette Cedex, France.
Evrin
Cécile
C
Briozzo
Pierre
P
Joly
Nathalie
N
Bârzu
Octavian
O
Gilles
Anne-Marie
AM
D000494:Allosteric Regulation / Q000502:physiology; D020816:Amino Acid Motifs / Q000502:physiology; D001665:Binding Sites; D019281:Dimerization; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D006160:Guanosine Triphosphate / Q000737:chemistry*; D009703:Nucleoside-Phosphate Kinase / Q000737:chemistry*; D020836:Protein Structure, Quaternary / Q000502:physiology; D014500:Uracil Nucleotides / Q000737:chemistry
D029968:Escherichia coli Proteins; D014500:Uracil Nucleotides; D006160:Guanosine Triphosphate; C023276:uridine monophosphate kinase; D009703:Nucleoside-Phosphate Kinase